Re: [gmx-users] query on plotting dynamical quantity

[jagannath mondal]

Hi Tsjerk
  Thanks for your suggestion on putting the parameters in bfactor column of
pdb. However, for this, the file format has to be a pdb format. However, if
I have a trajectory ( in xtc format) and each frame's 'bfactor' values are
getting updated, then do I need to convert entire xtc files into pdb files
for visualization?
Jagannath


On Tue, Mar 8, 2016 at 12:43 PM, Tsjerk Wassenaar  wrote:

> Hi Jagannath,
>
> Convert the file to PDB format and write the values to the b-factor field.
> Most visualization programs can color by b-value.
>
> Cheers,
>
> Tsjerk
> On Mar 8, 2016 06:50, "Jagannath Mondal"  wrote:
>
> > Dear gromacs-users
> >
> >   I am sorry to write you a visualization-related query. I hope you can
> > help.
> >
> > My query is: How can I visualize a trajectory file ( example in vmd)
> where
> > I have an extra 4th column ( apart from x y z which are first 3 columns)
> > which has a dynamically changing variable for each particles ? The plan
> is
> > to color gradient the atoms using the values of   4th column.
> >
> >
> > Is there a way to do it. I am sorry again to write you off the list.
> >  Here is an excerpt from first few lines:
> > Jagannath
> >
> >219GLN  C  186.961000 4.468000 3.7760001.678980
> >
> > 220LEU  C  376.753000 4.257000 3.98  6.526284
> >
> > 221THR  C  516.618000 4.023000 4.151000  11.323132
> >
> > 222ALA  C  616.565000 3.742000 4.306000  26.957896
> >
> > 223ALA  C  716.409000 3.464000 4.313000  52.708403
> >
> > 224GLN  C  886.213000 3.54 4.528000
> > --
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Re: [gmx-users] Unable to visualize my Polymer chains in VMD software generated using RIS theory in a proper way

[Abhishek Gupta]

Dear GROMACS Users,

I am trying to visualize the simple polyethylene chains (multiple chains)
consisting of certain number of atoms generated using RIS theory using VMD.
I'm using the PDB format to express coordinates to visualize my chains. The
chains are very random and at some points multiple atoms of a chain comes
very near to each other. Sometimes, even there is inter chain overlapping
and multiple atoms of different chains comes in close vicinity of each
other. In such a situation, while visualizing via. VMD, there appears a
bond between those close or very close atoms within a chain or between two
chains. Therefore, the visulaization by VMD shows that number of bonds is
much greater than the number of atoms and forms a cage like structure (in
some cases) between the closely spaced or overlapping atoms. What might be
the possible cause of this ? Does VMD connects Atoms taking in some
distance criterion ? Can we change that distance criteria that VMD utilize
to connect the atoms of a polymer chain in succession ?

Thanks and Regards--
Abhishek
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[gmx-users] Optimal hardware for running Gromacs

[David Berquist]

I'm looking into building a desktop computer for running Gromacs
simulations.  I'd like to know how I should configure it to get the best
performance possible for the price.

One example of something I might run on this system would be: simulate an
ionic polymer of approximately 100k atoms for 1 millisecond.  Coarse
grained atoms, using Martini force field.

I would be planning to spend something under $1500 on this system.



In regards to the graphics card, what factors are important?  I assume that
the single precision Flop/s are a big factor, but what about memory
bandwidth(on the card itself)?

I've noticed that Gromacs pages on GPUs tend to recommend nVidia cards,
specifically those with CUDA Compute Capability 5.2.  But, AMD Radeon cards
appear to offer the same processing power for far lower prices(or
alternatively, significantly more processing power for the same price).

For example, the nVidia GTX 970 offers 3494 GFlop/s of single precision,
and 109 GFlop/s of double precision.  It currently costs $290 at Newegg.
On the other hand, the AMD Radeon R9 380 provides 3476.5 GFlop/s single
precision, and 217.3 GFlop/s of double precision.  It currently costs $150
on Newegg.

That's practically the same single precision, and nearly double the
double-precision for around half the price.

Or, for about the same price as the nVidia GTX 970 I could get an AMD
Radeon R9 390.  It provides 5120 GFlop/s of single precision and 640
GFlop/s of double precision.  That costs $310 on Newegg.

That is, on paper, 46.5% more single precision performance, and 487% more
double precision performance(nearly 5 times as much) for only a 6.9% higher
price.

So, does Gromacs run a lot faster on nVidia GPUs?  Would the nVidia GTX 970
provide similar or better performance than the AMD Radeon R9 390?

One more GPU Question; does Gromacs scale linearly across multiple graphics
cards?   So, if I have two identical cards which offer 2000 GFlop/s
performance each, would they both together perform about the same as a
more-expensive single card which provides 4000GFlop/s(provided you have a
fast enough CPU, of course)?



Now, how about the CPU performance?  Would it be better to spend a lot of
my budget on a high-end GPU, and then go for a low cost CPU?  Something
like an  AMD Athlon X4 860K Kaveri Quad-Core 3.7 GHz CPU?  Or would
something like that bottleneck the performance of an nVidia GTX 970 or GTX
980?  Maybe a AMD FX-6300 Vishera 6-Core 3.5 GHz?  AMD FX-8300 Vishera
8-Core 3.3GHz?
Does Intel vs AMD make any significant difference?  When running Gromacs on
a system with GPU compute turned on, what sort of computing load does
Gromacs put on the CPU?  Is there any commonly used CPU benchmark that can
be used to approximate relative Gromacs performance between CPUs?



How important is the system RAM speed?  Should I spend more of my budget
building a DDR4 system(more expensive CPU, motherboard, and RAM modules),
or would that not make a significant difference over DDR3?

Would you happen to know what quantity of memory should be sufficient for
common Gromacs simulation runs, or runs such as the example I included
above?


Finally, does the speed of the hard drive impact Gromacs performance?  The
options are a cheap spinning-platter hard drive(100-200MB/s sequential
write), a low-cost SSD(400-500MB/s sequential write), or a high-speed PCI-E
SSD(1000-1500MB/s sequential write).  Would writing out the data(.xtc,
.trr, .edr) to a slower hard drive(100-200MB/s sequential write speed)
cause the Gromacs simulation to slow down?
I don't see any reason that a cheap spinning platter hard drive would slow
Gromacs simulations down, but I want to make sure I'm not missing
anything.

Thank you for your time.  I'd be very grateful for any information you can
give me, or direct me to.

David Berquist
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[gmx-users] How to Search Forums and Creating Binary from Existing Topology/Trajectory File

[Robert Molt]

Good evening,

I have two questions, one general, one specific.

The big question is that I do not understand how to search the GROMACS 
forums efficiently. The search bar on 
(http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List) allows a 
search to be conducted, but the links shown do not seem to be of the 
user forums and are very slow to load when selected. I can see the grand 
list of all messages on 
(https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/) but it's 
not clear to me how to search it for a particular string.


The specific reason I wanted to search the forums was to answer a very 
specific question. I may as well pose it here, as well. I have converted 
an Amber trajectory into the GROMACS form; I have also converted an 
Amber parameter file to a GROMACS form. I would like to create a GROMACS 
binary (tpr file).


1.) From what I have gleamed from tutorials, I need to use a variant of 
the pdb2gmx command (presumably not for a pdb, but for a trajectory)?


2.) I also do not wish to use the methods of various tutorials like 
(http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme_old/index.html) 
in terms of loading an existing force field; the parameters I have were 
developed in-house. I thus would like to load my 
converted-from-Amber-to-Gromacs topology file. Instead of the -ff flag, 
what flag indicates use of an existing parameter file?


3.) An important caveat: I have to use the 4.5 version of Gromacs. I 
hope the commands are all the same, since I know the current version of 
Gromacs is 5.0


Thank you for your time

--
Dr. Robert Molt Jr.
r.molt.chemical.phys...@gmail.com

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Re: [gmx-users] gmx analyze (5.1.2) correlation function(s)

[João Henriques]

I've encountered this issue:

http://bugzilla.gromacs.org/issues/1914

Looked like it at first, but then I noticed that I am not using
-nonormalize, i.e. I am normalizing by default.

J

On Fri, Mar 11, 2016 at 3:26 PM, João Henriques <
joao.henriques.32...@gmail.com> wrote:

> Dear all,
>
> Does gmx analyze, version 5.1.2, contain any known bug/problem that I am
> not aware of? I recently moved from gromacs 4.6.7 to 5.1.2 and I seem to
> have encountered an issue with the calculation and/or output of the
> (auto)correlation function(s). It basically outputs all zeros on the second
> column of the output xvg file, whereas when I use g_analyze 4.6.7 I get the
> normal behavior, i.e. a beautiful autocorrelation function.
>
> Thank you in advance,
> Cheers,
> J
>
>
>
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[gmx-users] gmx analyze (5.1.2) correlation function(s)

[João Henriques]

Dear all,

Does gmx analyze, version 5.1.2, contain any known bug/problem that I am
not aware of? I recently moved from gromacs 4.6.7 to 5.1.2 and I seem to
have encountered an issue with the calculation and/or output of the
(auto)correlation function(s). It basically outputs all zeros on the second
column of the output xvg file, whereas when I use g_analyze 4.6.7 I get the
normal behavior, i.e. a beautiful autocorrelation function.

Thank you in advance,
Cheers,
J
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Re: [gmx-users] Query regarding energy minimization step (step 12: Water molecule starting at atom 13529 can not be settled.)

[Justin Lemkul]

On 3/11/16 2:50 AM, shrikant kaushik wrote:

Dear all gromacs users,
   [shrikant@Ares Simulation]$ gmx-5.1.2
mdrun -v -deffnm em
:-) GROMACS - gmx mdrun, VERSION 5.1.2 (-:

 GROMACS is written by:
  Emile Apol  Rossen Apostolov  Herman J.C. BerendsenPar
Bjelkmar
  Aldert van Buuren   Rudi van Drunen Anton Feenstra   Sebastian Fritsch
   Gerrit Groenhof   Christoph Junghans   Anca HamuraruVincent Hindriksen
  Dimitrios KarkoulisPeter KassonJiri Kraus  Carsten
Kutzner
 Per Larsson  Justin A. Lemkul   Magnus Lundborg   Pieter Meulenhoff
Erik Marklund  Teemu Murtola   Szilard Pall   Sander Pronk
Roland Schulz Alexey Shvetsov Michael Shirts Alfons Sijbers
Peter TielemanTeemu Virolainen  Christian WennbergMaarten Wolf
and the project leaders:
 Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel

Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2015, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.

GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.

GROMACS:  gmx mdrun, VERSION 5.1.2
Executable:   /usr/local/gromacs-5.1.2/bin/gmx-5.1.2
Data prefix:  /usr/local/gromacs-5.1.2
Command line:
   gmx-5.1.2 mdrun -v -deffnm em


Running on 1 node with total 4 cores, 4 logical cores
Hardware detected:
   CPU info:
 Vendor: GenuineIntel
 Brand:  Intel(R) Core(TM) i5-2400 CPU @ 3.10GHz
 SIMD instructions most likely to fit this hardware: AVX_256
 SIMD instructions selected at GROMACS compile time: AVX_256

Reading file em.tpr, VERSION 5.1.2 (single precision)
Using 1 MPI thread
Using 4 OpenMP threads


Steepest Descents:
Tolerance (Fmax)   =  1.0e+03
Number of steps=5
Step=0, Dmax= 1.0e-02 nm, Epot=  1.64486e+07 Fmax= 3.27208e+07, atom=
4176
Step=1, Dmax= 1.0e-02 nm, Epot=  1.55865e+07 Fmax= 3.13386e+07, atom=
4176
Step=2, Dmax= 1.2e-02 nm, Epot=  1.46513e+07 Fmax= 2.97319e+07, atom=
4176
Step=3, Dmax= 1.4e-02 nm, Epot=  1.36016e+07 Fmax= 2.78772e+07, atom=
4176
Step=4, Dmax= 1.7e-02 nm, Epot=  1.24230e+07 Fmax= 2.57543e+07, atom=
4176
Step=5, Dmax= 2.1e-02 nm, Epot=  1.3e+07 Fmax= 2.33503e+07, atom=
4176
Step=6, Dmax= 2.5e-02 nm, Epot=  9.67180e+06 Fmax= 2.06643e+07, atom=
4176
Step=7, Dmax= 3.0e-02 nm, Epot=  8.12309e+06 Fmax= 1.77136e+07, atom=
4176
Step=8, Dmax= 3.6e-02 nm, Epot=  6.50058e+06 Fmax= 1.45408e+07, atom=
4176
Step=9, Dmax= 4.3e-02 nm, Epot=  4.86276e+06 Fmax= 1.12217e+07, atom=
4176
Step=   10, Dmax= 5.2e-02 nm, Epot=  3.30460e+06 Fmax= 7.87434e+06, atom=
4176
Step=   11, Dmax= 6.2e-02 nm, Epot=  2.04717e+06 Fmax= 9.25255e+06, atom=
75560
Wrote pdb files with previous and current coordinates

---
Program gmx mdrun, VERSION 5.1.2
Source code file:
/usr/local/src/gromacs-5.1.2/src/gromacs/mdlib/constr.cpp, line: 555

Fatal error:

step 12: Water molecule starting at atom 13529 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---


http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System

Since it's EM that's failing, the most likely problem is unreasonable 
coordinates (mdrun is printing out likely locations of these nasty 
interactions!).  Since you've provided no other useful information about what 
you're doing or what your system is, that's the best advice that can be given.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] Syntax error - File lig.prm, line 2 Last line read:

[Justin Lemkul]

On 3/11/16 1:38 AM, Nikhil Maroli wrote:

Problem solved,

Keeping the ligand topology right after the ff.itp


For posterity, I will point out that this is precisely what is intended by the 
statement:


"The force field has to be fully constructed before any molecules can be 
defined."

on the page that I linked.  I think I will amend that page to be a bit more 
generic.  The error is often encountered with [atomtypes] but any bonded or 
nonbonded directive will trigger the same error.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] Regarding energy calculation of head groups

[Justin Lemkul]

On 3/11/16 12:20 AM, Raju Lunkad wrote:

Dear all Gromacs users,
I wanted to calculate the enthalpy of headgroups of the surfactants. In
"mdp file" I have mentioned the energy as N4_O2 (Surfactants head groups)
but I am getting the following error:

  atoms 1 and 4 in charge group 1 of molecule type 'BTM' are in different
energy groups

I am not sure but in my opinion,  the error is coming because of the N4
contains  -0.5 charge and O2 contains -0.7 charge.
Kindly tell me how to mention energy groups in "mdp file" with charged
atoms.



The error has nothing to do with charge.  The energygrps you defined are 
splitting a charge group, which is not something you can do.  I also don't know 
what value there would be in calculating the enthalpy of part of a larger 
molecule, but that's for you to decide...


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] Regarding 2D simulation

[Catarina A. Carvalheda dos Santos]

Go to http://manual.gromacs.org/online/mdp_opt.html and search for "pbc".






On 11 March 2016 at 05:22, Raju Lunkad 
wrote:

> Dear all Gromacs users,
>
> I am running the simulation using pbc in 2 directions instead of all
> directions. For example, pbc = xy instead of pbc = xyz.
> Kindly tell me how to run the simulation using pbc in two directions.
>
> Best Regards,
> Raju Lunkad
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>
> The University of Dundee is a registered Scottish Charity, No: SC015096
>



-- 
Catarina A. Carvalheda

PhD Student
Computational Biology Division
SLS & SSE
University of Dundee
DD1 5EH, Dundee, Scotland, UK
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[gmx-users] I have a question about 'How h_bond module in Groamcs compute Hydrogen bond correlation function '

[자연과학부]

Hello, I'm an user of Gromacs who want to calculate hydrogen bond life time in 
various system. I know that we can use h_bond module with -ac option to get 
hydrogen bond lifetime between two groups but I want to make sure that how 
those correlation function comes out.


I analyzed trajectroy of each  hydrogen pairs and I could make existence 
function ( h(t) ) for each tagged h_bond pair and I computed correlation 
function but It shows different pattern from I got from -ac option.


Can anybody tell me how hydrogen bond correlation function is computed in 
Gromacs from trajectroy?


I read paper of Luzar ,Chandler and Van der Spoel more than 10 times and I know 
all those definition. What I want to know is how practically we can compute it.


Thank you for reading my message!!!


Sincerely, Ho Yong
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